Hypoxia inducible factor-1alpha (HIF-1alpha) plays an important role in maintaining oxygen equilibrium. Pathologic conditions such as hypoxia or ischemia have been reported to cause cellular apoptosis as well as to regulate HIF-1alpha. However, the relationship between HIF-1alpha and neuronal apoptosis in neonatal rats with hypoxia-ischemia brain injury is unclear. We hypothesized that HIF-1alpha will be differentially regulated depending upon the stimuli, such as hypoxia alone versus hypoxia-ischemia (HI), and thus play a role in neuronal apoptosis in developing rat brain. To test this hypothesis, we subjected postnatal day 10 (P10) rats to either hypoxia (8%O(2) and 92%N(2) for 2.5 h) or HI (ligating the right common carotid artery followed by hypoxia). Rat brains from hypoxia, HI, and sham controls were collected to detect HIF-1alpha expression and cellular apoptosis using immunohistochemistry, Western blot analysis, and TdT-mediated dUTP-biotin nick end labeling (TUNEL). We found that HIF-1alpha expression was upregulated at 4 h, peaked at 8 h, and declined at 24 h after hypoxia/HI compared with sham controls. Moreover, HIF-1alpha expression was significantly stronger in hypoxia-alone-treated rats than that in HI-treated rats. Meanwhile, we found that cellular apoptosis was more severe in HI-treated rats than that in hypoxia-treated rats. Furthermore, cellular apoptosis was prominent at 24 h in either hypoxia or HI but more severe in HI-treated rats. Our findings that cellular apoptosis increases with downregulation of HIF-1alpha suggest that HIF-1alpha may play a protective role in regulating cellular apoptosis in neonatal hypoxia-ischemia brain damage (HIBD).